boolean modifier leaves cutting edge on face
If you want to convert that Ngon into quads delete it and use Ctrl+E > Bridge Edge Loops; it should work nicely if amount of vertices is the same.



However you can use more convenient way in order to construct cylinder like on your screenshot. 


Start with simple cylinder, select its top and bottom faces (Ngons) and  inset them. Press I and drag the mouse to change effect.
With both Ngons still selected use Bridge Edge Loops.